Advances to tackle backbone flexibility in protein docking
نویسندگان
چکیده
منابع مشابه
Protein-protein docking with backbone flexibility.
Computational protein-protein docking methods currently can create models with atomic accuracy for protein complexes provided that the conformational changes upon association are restricted to the side chains. However, it remains very challenging to account for backbone conformational changes during docking, and most current methods inherently keep monomer backbones rigid for algorithmic simpli...
متن کاملModeling backbone flexibility improves protein stability estimation.
In designing mutagenesis experiments, it is often crucial to know how certain mutations will affect the structure and thermodynamic stability of the protein. Here, we present a methodology, Eris, to efficiently and accurately compute the stability changes of proteins upon mutations using our protein-modeling suite, Medusa. We evaluate the stability changes upon mutations for 595 mutants from fi...
متن کاملAutoDockFR: Advances in Protein-Ligand Docking with Explicitly Specified Binding Site Flexibility
Automated docking of drug-like molecules into receptors is an essential tool in structure-based drug design. While modeling receptor flexibility is important for correctly predicting ligand binding, it still remains challenging. This work focuses on an approach in which receptor flexibility is modeled by explicitly specifying a set of receptor side-chains a-priori. The challenges of this approa...
متن کاملAdvances and Challenges in Protein-Ligand Docking
Molecular docking is a widely-used computational tool for the study of molecular recognition, which aims to predict the binding mode and binding affinity of a complex formed by two or more constituent molecules with known structures. An important type of molecular docking is protein-ligand docking because of its therapeutic applications in modern structure-based drug design. Here, we review the...
متن کاملIncorporating Backbone Flexibility in MedusaDock Improves Ligand-Binding Pose Prediction in the CSAR2011 Docking Benchmark
Solution of the structures of ligand-receptor complexes via computational docking is an integral step in many structural modeling efforts as well as in rational drug discovery. A major challenge in ligand-receptor docking is the modeling of both receptor and ligand flexibilities in order to capture receptor conformational changes induced by ligand binding. In the molecular docking suite MedusaD...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
ژورنال
عنوان ژورنال: Current Opinion in Structural Biology
سال: 2021
ISSN: 0959-440X
DOI: 10.1016/j.sbi.2020.11.011